Method for controlling base sequence determination, base sequence determination system and control device

ABSTRACT

The present disclosure discloses a method for controlling a base sequence determination, a base sequence determination system, and a control device. The base sequence determination system includes a fluid device and an optical device, a reaction device includes a first component and a second component, and a repeated executable unit included in the base sequence determination is defined as: a second biochemical reaction—a first biochemical reaction—photographing. The method includes, after initiation steps are completed, using the fluid device to perform the second biochemical reaction and the first biochemical reaction of the sample on the first component, while using the optical device to photograph the sample on the second component. The initial steps include: a. using the fluid device to perform the first biochemical reaction of the sample on the first component, b. using the optical device to photograph the sample on the first component after the first biochemical reaction, and c. using the fluid device to perform the first biochemical reaction of the sample on the second component. The above-mentioned method can improve the efficiency of base sequence determination.

CROSS REFERENCE TO RELATED APPLICATION

This application claims the benefit under 35 U.S.C. 119(a)-(d) toChinese Application No. 201611259507.4, filed Dec. 30, 2016, whichapplication is hereby incorporated by reference in its entirety.

TECHNICAL FIELD

The present disclosure relates to the field of sequencing techniquesand, more particularly, to a method for controlling base sequencedetermination, a base sequence determination system and a control devicefor controlling base sequence determination.

BACKGROUND

Sequence determination, i.e., sequencing, includes determination ofnucleic acid sequences. Sequencing platforms currently available in themarket include generations I, II, and III of sequencing platforms.

From the point of view of functional control, the sequencing instrumentincludes a detection module and utilizes the detection module totransform and/or collect varied information in the biochemical reactionsin sequencing to determine the sequence. The detection module generallyincludes an optical detection module, a current detection module and aacid-base (pH) detection module. The sequencing platform based on theoptical detection principle is used for sequence determination byanalyzing variation in the optical signals collected from a sequencingbiochemical reaction.

SUMMARY OF THE INVENTION

An embodiment of the present disclosure is intended to at least solveone of the technical problems present in the related art or at leastprovide an alternative practical solution. To this end, the embodimentof the present disclosure provides a method, a sequence determinationsystem, and a control device for controlling the base sequencedetermination.

An embodiment of the present disclosure provides a method forcontrolling base sequence determination, wherein the base sequencedetermination includes a first biochemical reaction, a secondbiochemical reaction, and photographing, the first biochemical reactionand the second biochemical reaction are carried out on a reactiondevice, and a sequence determination system is configured to control thebase sequence determination, the sequence determination system includesa fluid device and an optical device, the reaction device is connectedto the fluid device; the reaction device includes a first component anda second component, a subject sample being placed on each of the firstcomponent and the second component; and, a repeated executable unitcomprised in the base sequence determination is defined as: a secondbiochemical reaction—a first biochemical reaction—photographing; whereinthe method comprises, after completion of following initial steps, whenone of the first component and the second component is subjected to thesecond biochemical reaction and the first biochemical reaction of thesample by using the fluid device, photographing the sample in the othercomponent with the optical device, and wherein the initial stepsinclude:

a. using the fluid device to perform the first biochemical reaction ofthe sample on one of the first component and the second component, b.using the optical device to photograph the sample on the component afterthe first biochemical reaction, and c. using the fluid device to performthe first biochemical reaction of the sample on another one of the firstcomponent and the second component.

In the above-described method, the reaction device is divided into atleast two components, and one of the components is subjected to abiochemical reaction by the fluid device while another one of thecomponents is photographed, i.e., has its image acquired by the opticalmeans, thereby reducing the sequencing time and improving the sequencingefficiency.

An embodiment of the present disclosure provides a sequencedetermination system for controlling base sequence determination,wherein the base sequence determination comprises a first biochemicalreaction, a second biochemical reaction, and photographing, wherein thefirst biochemical reaction and the second biochemical reaction takeplace on a reaction device, wherein the sequence determination systemcomprises a control device, a fluid device and an optical device, thereaction device being connected to the fluid device; the reaction devicecomprises a first component and a second component, a subject samplebeing placed on each of the first component and the second component;and, a repeated executable unit comprised in the base sequencedetermination is defined as: a second biochemical reaction—a firstbiochemical reaction—photographing; the control device being configuredto, after completion of following initial steps, when one of the firstcomponent and the second component is subjected to the secondbiochemical reaction and the first biochemical reaction of the sample byusing the fluid device, photographing the sample in the other componentwith the optical device, and wherein the initial steps comprise:

a. utilizing the fluid device, by the control device, to perform thefirst biochemical reaction of the sample on one of the first componentand the second component, b. utilizing the optical device, by thecontrol device, to photograph the sample on the component after thefirst biochemical reaction, and c. utilizing the fluid device, by thecontrol device, to perform the first biochemical reaction of the sampleon another one of the first component and the second component.

In the above-described sequence determination system, when performingbase sequence determination, the reaction device is divided into atleast two components, and one of the components is subjected to abiochemical reaction by the fluid device while another one of thecomponents is photographed, i.e., has its image acquired by the opticalmeans, thereby reducing the sequencing time and improving the sequencingefficiency.

A control device for controlling base sequence determination for use ina sequence determination system according to an embodiment of thepresent disclosure is provided, the sequence determination systemcomprising a fluid device and an optical device, wherein the controldevice comprises: a storage device for storing data, the data comprisinga computer executable program; and a processor for executing thecomputer executable program, wherein the executing the computerexecutable program comprises performing the above-described method.

A computer-readable storage medium according to an embodiment of thepresent disclosure is provided for storing a computer executableprogram, executing the program comprising executing the above-describedmethod. The computer-readable storage medium may include read-onlymemory, random access memory, magnetic disks, or optical disks.

Additional aspects and advantages of the embodiments of the presentdisclosure will be set forth in part in the description which follows,and in part will be apparent from the following description, or may belearned by practice of the embodiments of the disclosure.

BRIEF DESCRIPTION OF THE DRAWINGS

The foregoing and/or additional aspects and advantages of theembodiments of the present disclosure will become apparent and readilyappreciated from the following description of the embodiments when takenin conjunction with the accompanying drawings in which:

FIG. 1 is a schematic flow diagram of a method for controlling basesequence determination according to an embodiment of the presentdisclosure.

FIG. 2 is a schematic structural view of a fluid device according to anembodiment of the present disclosure.

FIG. 3 is a schematic block view of an optical device according to anembodiment of the present disclosure.

FIG. 4 is another schematic block view of an optical device according toan embodiment of the present disclosure.

FIG. 5 is a block diagram of a sequence determination system accordingto an embodiment of the present disclosure.

DETAILED DESCRIPTION OF THE EMBODIMENTS

Embodiments of the present disclosure are described in detail below,examples of which are shown in the accompanying drawings, wherein likeor similar reference numerals refer to like or similar elements orelements having the same or similar functions throughout. Theembodiments described below with reference to the accompanying drawingsare exemplary only and are for the purpose of explaining the disclosureand are not to be construed as limiting the disclosure.

In the description of the present disclosure, it is to be understoodthat the terms “first” and “second” are for illustrative purposes onlyand are not to be construed as indicating or imposing a relativeimportance or implicitly indicating the number of technical featuresindicated. Thus, a feature that is defined with the term “first” or“second” may expressly or implicitly include one or more of thefeatures. In the description of the present disclosure, the meaning of“plurality” is two or more, unless otherwise specifically defined.

In the description of the present disclosure, it is to be understoodthat, unless otherwise expressly stated and defined, “connection” shouldbe broadly understood. For example, it may be a fixed connection, adetachable connection, or an integral connection; it may be a mechanicalconnections, a electrical connection, or intercommunication; and it maybe direct connection, indirect connection through an inter medium, orinternal communication or interaction between two elements. The specificmeaning of the above-mentioned terms in the present disclosure can beunderstood by those skilled in the art in light of specificcircumstances.

The following disclosure provides a number of different embodiments orexamples for implementing the different structures of the presentdisclosure. In order to simplify the disclosure of the presentdisclosure, components and settings of specific examples will bedescribed below. In addition, the present disclosure may repeat thereference numerals and/or reference numerals in different examples forthe sake of simplicity and clarity, which in itself does not indicatethe relationship between the various embodiments and/or settingsdiscussed.

The “sequencing” or “sequence determination” as used in the embodimentsof the present disclosure refers to nucleic acid sequencing, includingDNA sequencing and/or RNA sequencing, including long fragment sequencingand/or short fragment sequencing. The so-called “base sequencedetermination” refers to sequencing. In general, in the determination ofa nucleic acid sequence, a base or a specific type of base can bedetermined by a cycle of sequence determination, wherein the base isselected from at least one of A, T, C, G and U. In the sequencing bysynthesis, and/or in the sequencing by litigation, said one cycle ofsequence determination reaction includes an extension reaction (baseextension), information collection (photograph/image acquisition), andgroup cleavage. The term “nucleotide analog”, i.e., substrates, is alsoknown as a terminator, which is an analog of A, T, C, G and/or U and iscapable of pairing with a particular type of base following theprinciple of base complementation pairing and inhibiting the binding ofthe next nucleotide (analog)/substrate to the template strand.

Referring to FIG. 1, an embodiment of the present disclosure provides amethod for controlling base sequence determination. The base sequencedetermination comprises a first biochemical reaction, a secondbiochemical reaction and photographing, wherein the first biochemicalreaction and the second biochemical reaction are carried out in thereaction device 40, and the base sequence determination is controlled bya sequence determination system.

Referring to FIGS. 2 and 3, the sequence determination system comprisesa fluid device 100 and an optical device 200, the reaction device 40being connected to the fluid device 100; the reaction device 40comprises a first component 41 and a second component 42, a subjectsample being placed on each of the first component and the secondcomponent; and, a repeated executable unit S12 comprised in the basesequence determination is defined as: a second biochemical reaction—afirst biochemical reaction—photographing;

wherein the method comprises, after completion of following initialsteps S11, when using the fluid device to make one of the firstcomponent 41 and the second component 42 be subjected to the secondbiochemical reaction and the first biochemical reaction of the sample,using the optical device 200 to photograph the sample in the othercomponent, and wherein the initial steps include:

a. using the fluid device 100 to perform the first biochemical reactionof the sample on one of the first component 41 and the second component42,

b. using the optical device 200 to photograph the sample on thecomponent after the first biochemical reaction, and

c. using the fluid device 100 to perform the first biochemical reactionof the sample on another one of the first component 41 and the secondcomponent 42.

In the above-described method, the reaction device is divided into atleast two components base on the base sequence determination, and one ofthe components is subjected to a biochemical reaction using the fluiddevice 100 while another one of the components is photographed, i.e.,has its image acquired using the optical means 200, thereby reducing thesequencing time and improving the sequencing efficiency.

In particular, the inventors, based on the discovery of the timedifference between the biochemical reaction and the informationcollection in the base sequence determination, the reaction device andthe number of the optical devices in the sequence determination system,divide the reaction device into at least two components and design theafore-mentioned computer-executable method to perform complete orpartial sequence determination reaction by parallel controlling andcalling of the entire or partial device/system. As a result, the timedifferences among the main steps of the base sequence determination aresufficiently utilized and the reaction efficiency greatly improved.

In general, considering the device/system required for sequencedetermination reaction in terms of hardware costs, the cost of theoptical device/system is greater than the cost of the fluiddevice/system, and the cost of the fluid device/system is greater thanthe cost of the reaction device/chip. By using the method of the presentdisclosure to control the base sequence determination, it is possible tomake full use of the optical device/system, the fluid device/the system,and the reaction device to further reduce the sequencing cost.

In particular, in some embodiments, the reaction device 40 may be achip, the first component 41 and the second component 42 of the reactiondevice 40 can each include a plurality of channels. After the initialsteps S11, the channel of the first component 41 and the channel of thesecond component 42 are staggered, unsynchronized, and unaffected in thebase sequence determination. For example, when the sample on the firstcomponent 41 is subjected to a biochemical reaction, the fluid device100 delivers the reagent for the reaction to the first component 41, atwhich time the same reagent does not enter the second component 42, andvice versa.

In one example, nucleic acid sequence determination is performed on asingle molecule sequencing platform using total internal reflection(TIRF) optical system for detection; and, based on the empirical valuesfor the amount of data for subsequent genetic information analysis andthe ratio of the valid data after processing, the amount of raw datarequired for estimation is estimated to be approximately 300 fields ofview (FOV). In one cycle of sequence determination reaction, the timerequired for controlling and moving the reaction device 40 andcollecting of 300 FOV using the optical device 200 is substantiallyequal to the total time of performing the first biochemical reaction andthe second biochemical reaction using the fluid device 100. The methodof this embodiment of the disclosure can improve the reaction efficiencyby double.

It will be appreciated by those skilled in the art that in some othercases, the amount of data required for genetic information analysis isreduced and/or the ratio of valid data after processing is increased, sothat the number of FOVs required for each cycle of sequencedetermination reactions is reduced, that is, the time required forphotographing is reduced or the total time of the biochemical reactionis prolonged. If so, then m reaction devices can be divided into ncomponents by the method of the present disclosure, wherein m and n areeach integers greater than or equal to 1 and n is greater than or equalto twice of m, so that the components are subjected to different stepsor stages of the same/different cycles of sequence determinationreaction, and the optical device 200 and the fluid device 100 can befully utilized to improve the reaction efficiency. It will also beappreciated by those skilled in the art that, in opposite direction ofthe above examples, such as the time required for biochemical reactionsreduces, the use of the method of the present disclosure can also takeadvantage of the number of components on the reaction device 40 toimprove efficiency.

In some embodiments, the sample to be sequenced has been immobilized onthe surface of the channels of the first component 41 and the secondcomponent 42 of the reaction device 40 prior to the base sequencedetermination. The sample to be sequenced is, for example, a samplehaving a double stranded or single stranded DNA chain.

In the embodiment of the present disclosure, the repeated executableunit S12 is the second biochemical reaction—the first biochemicalreaction—photographing, which refers to that, when performing the basesequence determination on a certain unit of the reaction device 40, thesample on the component is sequentially subjected to the secondbiochemical reaction, the first biochemical reaction and photographing.When the repeated executable unit is executed a plurality of times, themethod of the embodiment of the present disclosure will performrepetitive execution processes of the first biochemical reaction,photographing, and the second biochemical reaction of a sample on thecomponent, and/or the second biochemical reaction, the first biochemicalreaction and photographing of a sample on the component. It is to benoted that, generally, the base sequence determination is capable ofdetermining at least one base with each of the following cycle: thefirst biochemical reaction, the photographing and the second biochemicalreaction, wherein the base is selected from the group consisting of A,T, C, G, and U. It will be understood by those skilled in the art thatthe definition of a repeated executable units in the present disclosureis intended to facilitate description of the invention according to thedisclosure and does not limit the sequence of reactions in the basesequence determination.

In the embodiment of the present disclosure, when the sample on thefirst component 41 is subjected to the second biochemical reaction andthe first biochemical reaction using the fluid device 100, the sample onthe second component 42 is photographed by the optical device 200. Then,according to the repeated executable unit, after the second biochemicalreaction and the first biochemical reaction are performed on the sampleon the first component 41 using the fluid apparatus 100, the sample onthe first component 41 is photographed using the optical device 200;and, meanwhile, after the sample on the second component 42 isphotographed, the sample on the second component 42 is subjected to thesecond biochemical reaction and the first biochemical reaction by thefluid device 100.

In another embodiment, when the sample on the first component 42 issubjected to the second biochemical reaction and the first biochemicalreaction using the fluid device 100, the sample on the first component41 is photographed by the optical device 200. Then, according to therepeated executable unit, after the second biochemical reaction and thefirst biochemical reaction are performed on the sample on the secondcomponent 42 using the fluid apparatus 100, the sample on the secondcomponent 42 is photographed using the optical device 200; and,meanwhile, after the sample on the first component 41 is photographed,the sample on the first component 41 is subjected to the secondbiochemical reaction and the first biochemical reaction by the fluiddevice 100.

In the embodiment of the present disclosure, referring to FIG. 1, in theinitial steps S11,

a. using the fluid device 100 to perform the first biochemical reactionon the sample on the first component 41;

b. using the optical device 200 to photograph the sample on the firstcomponent 41 after the first biochemical reaction, and

c. using the fluid device 100 to perform the first biochemical reactionof the sample on the second component 42.

The initiation steps of another embodiment include:

a. using the fluid device 100 to perform the first biochemical reactionof the sample on the second component 42.

b. using the optical device 200 to photograph the sample on the secondcomponent 42 after the first biochemical reaction, and

c. using the fluid device 100 to perform the first biochemical reactionof the sample on the second component 42.

The image data is photographed by the optical device 200, and can beoutput to other devices/modules of the sequence determination system forprocessing to obtain a corresponding image.

In some embodiments, step a and step c are carried out simultaneously,or step b and step c are carried out simultaneously, or step b iscarried out before step c, or step b is carried out after step c. Assuch, the implementation of the method of controlling the sequencing hasmore flexibility.

Specifically, in the embodiment of the present disclosure, when thesample on the first component 41 is subjected to the first biochemicalreaction using the fluid device 100 in step a, the sample on the secondcomponent 42 is not affected by the first biochemical reaction of thesample on the first component 41, vice versa.

Preferably, steps b and c are carried out simultaneously, thus furtherimproving the efficiency of the method.

In some embodiments, the first biochemical reaction comprises anextension reaction, and the second biochemical reaction comprises groupcleavage. In this way, the method for controlling the base sequencedetermination may have a wider range of application.

In particular, in some embodiments, a sample to be sequenced, i.e., atemplate strand, has been fixed in the channels of the first component41 and the second component 42 of the reaction device 40 prior to thebase sequence determination. The polymerase/ligase extension reaction isbased on base complementation, incorporating specific substrates to thesample to be sequenced, and determining the type of substrateincorporated using a detectable group present on the substrate, so as todetermine the bases of to-be-sequenced sequence. In one example, thedetectable group includes a fluorescent group that emits fluorescence atthe excitation of a specific wavelength of laser light.

The cleavage reaction cleaves the group on the substrate incorporated tothe sample (template) to be sequestered, so that the next base of thetemplate can be continuously determined, i.e., the sample on the firstcomponent 41 and/or the second component 42 can continue with the basesequence determination.

In some embodiments, the extension reaction includes sequencing byligation and sequencing by synthesis.

In some embodiments, the second biochemical reaction comprises capping.The capping is mainly for the purpose of protecting the group/bond thatis exposed after the group cleavage. In one example, the firstbiochemical reaction comprises a base extension reaction in which thestructure of the substrate added is A/T/C/G-terminating group-linkingunit-light-emitting group, wherein the terminating group islight-cleavable and/or a chemically cleavable group, and the substrateis provided with a light-emitting group through a linker. The secondbiochemical reaction comprises group cleavage, wherein the exposed groupafter the removal of cleavable groups by light cleavage and/or chemicalcleavage is a mercapto group, and the mercapto group is protected fromoxidation by capping such as by adding an alkylating agent. In this way,the method of controlling the base sequence determination is wider inthe range of application.

In some embodiments, the photographing further includes adding animaging reagent. Said imaging reagent contains an antioxidant component,such as water-soluble vitamin E (Trolox), etc., to avoid or reduce thedamage or impact of light on the sample during the image acquisitionprocess.

Preferably, the light emitted by the laser excitated sample isfluorescent, which reduces the adverse effect of ambient light on theimage taken by the imaging device.

Further, one of the examples shows that the “signal collection” processincludes: addition of an imaging reagent, image acquisition (in theembodiment of the present disclosure, the addition of the imagingreagent occurs during the photographing); and after cleavage, washingwith a buffer (buffed), capping (addition with a protective reagentbased on the substrate structure), and then washing with buffer2(buffer1, 2 can be the same or different).

In some embodiments, referring to FIG. 2, the fluid device 100 includesa valve body assembly 10 and a drive assembly 50 that communicates withthe valve body assembly 10 through a reaction device 40. When using thefluid device 100 to perform a first biochemical reaction and/or a secondbiochemical reaction on the sample of the first component 41 and/or thesecond component 42, the valve body assembly 10 is configured to switchamong different reagents, and the drive assembly 50 causes the valvebody assembly 10 to output reagents to the first component 41 and/or thesecond component 42.

Thus, through the valve body assembly 10 and the drive assembly 50, itis possible to conveniently input different reagents required for thebase sequence determination to the first component 41 and/or the secondcomponent 42.

In particular, in embodiments of the present disclosure, the fluiddevice 100 includes a reagent assembly, wherein the reagent comprises afirst reagent, a second reagent, and a third reagent, and the reagentassembly comprises a first reagent bottle 11 containing the firstreagent, a second reagent bottle 12 containing the second reagent bottle12 and a third reagent bottle 13 containing the third reagent. The valvebody assembly 10 connects the first reagent bottle 11, the secondreagent bottle 12 and the third reagent bottle 13 through a conduit. Thevalve assembly 10 switches communication with the different reagentbottles so that the drive assembly 50 can extract the reagents from thereagent bottle in communication with the valve body assembly 10 to thefirst component 41 and/or the second component 42.

In some embodiments, the valve body assembly 10 includes a firstmulti-way valve 20 and a first three-way valve 30, the first multi-wayvalve 20 switching communication with the different reagents to thefirst three-way valve 30, the first three-way valve 30 outputs thereagent output from the first multi-way valve 20 to the first component41 and/or the second component 42. Thus, it is implemented by use of thefirst multi-way valve 20 and the first three-way valve 30 that the driveassembly 50 causes the valve body assembly 10 to output differentreagents to the first component 41 and/or the second component 42.

Specifically, in the embodiment of the present disclosure, the firstmulti-way valve 20 is connected to the first reagent bottle 11, thesecond reagent bottle 12, the third reagent bottle 13, and the firstthree-way valve 30, and the first multi-way valve 20 is configured tocommunication the first reagent bottle 11, the second reagent bottle 12or the third reagent bottle 13 with the first three-way valve 30. Thefirst three-way valve 30 is connected to the first component 41, thesecond component 42 and the first multi-way valve 20, and the firstthree-way valve 30 is configured to connect the first component 41 orthe second component 42 with the first multi-way valve 20.

In some embodiments, the first reagent is a sequencing reagent, thesecond reagent is group cleavage reagent, and the third reagent is animaging reagent. The first multi-way valve 20 includes a firstextraction port 21 connected to the first reagent bottle 11, a secondextraction port 22 connected to the second reagent bottle 12, a thirdextraction port 23 connected to the third reagent bottle 13, and anliquid outlet port 24. The liquid outlet port 24 communicates with thefirst extraction port 21, or the second extraction port 22, or the thirdextraction port 23. The sequencing reagent is a reagent comprising atleast a portion of the reactants for the extension reaction, forexample, such as a reagent including a substrate and apolymerase/ligase. The substrate carries a detectable group, such as afluorophore.

The first three-way valve 30 includes a liquid suction port 31, a firstdiverging port 32, and a second diverging port 33. The liquid suctionport 31 communicates with the first diverging port 32 or the seconddiverging port 33. The liquid suction port 31 communicates with theliquid outlet port 24. The first component 41 and the second component42 communicate with the first diverging port 32 and the second divergingport 33, respectively.

In the embodiment of the present disclosure, the first multi-way valve20 is a rotary valve. The first extraction port 21, the secondextraction port 22, and the third extraction port 23 surround the liquidoutlet port 24. The first extraction port 21, the second extraction port22 and the third extraction port 23 are connected to the liquid outletport 24 through a rotary conduit 25 which rotates around the liquidoutlet port 24. The rotary conduit 25 can be sequentially rotated to thepositions of the first extraction port 21, the second extraction port 22and the third extraction port 23 so that the liquid outlet port 24 canbe sequentially connected to the first reagent bottle 11, the secondreagent bottle 12, and the third The reagent bottle 13. That is, thereaction device 40 can obtain different reagents from the first reagentbottle 11, the second reagent bottle 12 and the third reagent bottle 13,respectively, thereby subjecting the sample to a first biochemicalreaction, a second biochemical reaction and photographing. In otherembodiments, the communication order between the liquid outlet port 24and the first extraction port 21, the second extraction port 22, and thethird extraction port 23 may not be limited.

In the embodiment of the present disclosure, when the liquid suctionport 31 of the first three-way valve 30 communicates with the firstdiverging port 32, the liquid suction port 31 is decoupled from thesecond diverging port 33, and vice versa. The liquid suction port 31 maybe connected to the first diverging port 32 or the second diverging port33 as required by the sequencing. That is, when the sample on the firstcomponent 41 is subjected to the second biochemical reaction and thefirst biochemical reaction, the first diverging port 32 is communicatedwith the liquid suction port 30 so that the liquid suction port 30provides the desired second reagent and first reagent to the firstcomponent 41 through the first diverging port 32. After acquiring thesecond reagent and the first reagent form the first component 41, thesecond diverging port 33 communicates with the liquid suction port 31 sothat the second component 42 obtains the third reagent, and the opticaldevice 200 can photograph the sample on the second component 42.

After the sample on the second component 42 is photographed, the secondcomponent 42 starts to obtain the second reagent and the first reagentthrough the liquid suction port 31 so that the sample on the secondcomponent 42 is subjected to the second biochemical reaction and thefirst biochemical reaction. After the second reagent and the firstreagent are acquired by the second component 42, the first divergingport 32 communicates with the liquid suction port 31, the firstcomponent 41 acquires the third reagent, and the optical device 200 mayphotograph the sample on the first component 41, thereby effectivelyreducing the time of sequence determination and improving the efficiencyof the same.

In some embodiments, the drive assembly 50 includes a first pump 51 thatcommunicates the valve body assembly 10 through a first component 41 anda second pump 52 that communicates the valve body assembly 10 through asecond component 42. When using the fluid device 100 to perform thefirst biochemical reaction and/or the second biochemical reaction withthe sample on the first component 41 and/or the second component 42, thefirst pump 51 is configured to cause the valve body assembly 10 tooutput the reagent to the unit 41, and/or the second pump 52 isconfigured to cause the valve body assembly 10 to output the reagent tothe second component 42.

In this way, the reagent output from the valve body assembly 10 can besupplied to the first component 41 and/or the second component 42 by thefirst pump 51 and the second pump 52, respectively, for ease ofoperation.

Specifically, the first pump 51 and the second pump 52 areconduit-connected to the first component 41 and the second component 42,respectively.

In the example of the present disclosure, the first pump 51 communicateswith the first diverging port of the first three-way valve through thefirst component 41, and the second pump 52 communicates with the seconddiverging port of the first three-way valve through the second component42. In operation, the first pump 51 supplies a negative pressure to thefirst component 41 so that the first component 41 sequentially acquiresthe second reagent and the first reagent to perform the secondbiochemical reaction and the first biochemical reaction. Afteracquisition of the second reagent and the first reagent, the first pump51 stops providing negative pressure, the second pump 52 provides anegative pressure to cause the second component 42 to acquire the thirdreagent, and the sample on the second component 42 is photographed usingthe optical device 200.

It is to be noted that when the sample on the first component 41 issubjected to the second biochemical reaction and the first biochemicalreaction, the liquid outlet port 24 is successively connected to thesecond extraction port 22 and the first extraction port 21 to extractthe second reagent and the first reagent. The liquid suction port 31communicates with the first diverging port 32. When the first pump 51provides negative pressure to the first component 41, the second reagentand the first reagent are allowed to enter the passage of the firstcomponent 41 successively.

After the second reagent and the first reagent are acquired by the firstcomponent 41, the first pump 51 stops providing negative pressure, theliquid outlet port 24 communicates with the third extraction port 23 toextract the third reagent. The liquid suction port 24 communicates withthe second diverging port 33. The second pump 52 provides a negativepressure to the second component 42 so that the third reagent enters thechannel of the second component 42, and the sample on the secondcomponent 42 is photographed with the optical device 200. Thus, thevalve assembly 10, the drive assembly 50, and the optical device 200cooperate to perform a second biochemical reaction and a firstbiochemical reaction of the sample on the first component 41 whilephotographing the sample on the second component 42, and vice versa.

In some embodiments, the fluid device 100 includes at least one firstcontainer and sequencing reagent allocation assembly 60. The reagentcomprises a sequencing reagent. When using the fluid device 100 toperform a first biochemical reaction and/or a second biochemicalreaction on the sample of the first component 41 and/or the secondcomponent 42, the sequencing reagent allocation assembly 60 outputs thesequencing reagent to the first container in communication with thevalve body assembly 10.

In this way, it is convenient to add the reagent for carrying out thebase sequence determination to the first component 41 and the secondcomponent 42.

In particular, in the example of the present disclosure, the firstcontainer is the first reagent bottle 11. In one example, the number offirst containers is more than one.

The sequencing reagent allocation assembly 60 includes a plurality ofsequencing reagent feed bottles 61, a second multi-way valve 62, asecond three-way valve 63, and a third pump 64. The plurality ofsequencing reagent feed bottles 61 are used to hold a plurality ofsequencing reagent stock, and the second multi-way valve 62 issimultaneously conduit-connected to a plurality of sequencing reagentfeed bottles 61 and to the second three-way valve 63. The secondthree-way valve 63 is also conduit-connected to the third pump 64 andthe first reagent bottle 11. The third pump 64 communicates with one ofthe sequencing reagent feed bottles 61 via the second three-way valve 63and the second multi-way valve 62. The first reagent bottle 11communicates with the third pump 64 via the second three-way valve 63.The third pump 64 is sequentially communicated with the plurality ofsequencing reagent feed bottles 61 to extract the sequencing reagentstock in the plurality of sequencing reagent feed bottles 61 for mixingand formulating the sequencing reagent. The third pump 64 iscommunicated with the first reagent bottle 11 for injecting thesequencing reagent into the first reagent bottle 11.

In the present embodiment, the plurality of sequencing reagent feedbottles 61 contain different sequencing reagent stocks, respectively, sothat the third pump 64 can be used to sequentially extract thesequencing reagent stocks from the plurality of sequencing reagent feedbottles 61 so as to mix and formulating the sequencing reagent.

In one example, the number of sequencing reagent feed bottles 61 isnine, each containing solutions of different types of nucleoside analogs(substrates), DNA polymerase solutions, and various buffer solutions orcomponents of the mercapto protecting solution. The plurality ofsequencing reagent feed bottles 61 may be placed on a tube rack tosecure the plurality of sequencing reagent feed bottles 61. The sixsequencing reagent feed bottles 61 can also be labeled to facilitatesubsequent addition of sequencing reagent stocks and avoidcross-contamination of the sequencing reagent stocks. In otherembodiments, the number of sequencing reagent feed bottles 61 may alsobe two, three, four, five, six, seven, or eight other quantities, whichcan be adjusted depending on the actual needs and the characteristics ofeach solution.

The second multi-way valve 62 has a structure that is configured in thesame manner as the first multi-way valve 62, except that the secondmulti-way valve 62 achieves that the third pump 64 is sequentiallycommunicated with the plurality of sequencing reagent feed bottles 61,and the second multi-way valve 62 selects one of the sequencing reagentfeed bottles 61 to communicate. By controlling the communication length,adjustment of the extraction amount of the sequencing reagent from thesequencing reagent feed bottle 61 by the third pump 64 can becontrolled. Thus, the sequencing reagent stocks from the plurality ofsequencing reagent feed bottles 61 can be proportionally arranged tomeet the sequence determination requirements.

The second three-way valve 63 has a structure that is configured in thesame manner as the first three-way valve 30. The second three-way valve63 can realize the communication between the third pump 64 and thesecond multi-way valve 62 so that the third pump 64 can extract thesequencing reagent stocks from the plurality of sequencing reagent feedbottles 61 to formulate a sequencing reagent. The second three-way valve63 enables the third pump 64 to communicate with the first reagentbottle 11 so that the third pump 64 can inject the formulated sequencingreagent into the first reagent bottle 11.

The third pump 64 may provide negative pressure to the plurality ofsequencing reagent feed bottles 61 via the second three-way valve 63 andthe second multi-way valve 62, to extract the sequencing reagents fromthe plurality of sequencing reagent feed bottles 61. The third pump 64may also provide a positive pressure to the first reagent bottle 11 viathe second three-way valve 63 so as to inject the sequencing reagentinto the first reagent bottle 11.

Further, a first mixer 65 is connected between the second three-wayvalve 63 and the first reagent bottle 11. The first mixer 65 is providedwith a plurality of first winding ducts 651 that are connected end toend with each other, communicating between the second three-way valve 63and the first reagent bottle 11.

In the embodiment of the present disclosure, the plurality of the firstwinding ducts 651 is fixed to a fixing plate. The first winding ducts651 are S-shaped, and the plurality of the winding ducts 651 may bejuxtaposed in multiple rows that are in communication with each other.The plurality of first winding ducts 651 are used for communicationbetween the second three-way valve 63 and the first reagent bottle 11 sothat the sequencing reagent injected from the third pump 64 is subjectto a buffer and extended flow path. As a result, the plurality ofsequencing reagent stocks in the sequencing reagents is sufficientlymixed to enhance the reaction efficiency of the sequencing reagent. Inother embodiments, the plurality of winding ducts 651 may also be coiledsequentially.

The number of the first reagent bottles 11 may be one or more than one.In one example, the number of the first reagent bottles 11 is more thanone and the solutions containing different types of substrates arestored separately. The sequencing reagent allocation assembly 60 alsoincludes a third multi-way valve 66 that is simultaneouslyconduit-connected to a plurality of first reagent bottles 11, and asecond three-way valve 63, wherein a third pump 64 is in communicationwith one of the first reagent bottles 11 via the second three-way valve63 and the third multi-way valve 66.

In the embodiment of the present disclosure, the sequencing reagents inthe plurality of first reagent bottles 11 are different, and the numberof the first reagent bottles 11 is four. Depending on the ratio of thesequencing reagent stocks of the plurality of sequencing reagent feedbottles 61 to be extracted by the third pump 64, different sequencingreagents may be formulated, so that the plurality of first reagentbottles 11 may be used to contain a plurality of different sequencingreagents. The third multi-way valve 66 is configured in the same manneras the structure of the second multi-way valve 62. The third multi-wayvalve 66 may enable the third pump 64 to sequentially inject differentsequencing reagents into the plurality of first reagent bottles 11,respectively. Specifically, each time a sequencing reagent isformulated, the third pump 64 selects a first reagent bottle 11 throughthe second three-way valve 63 and the third multi-way valve 66, andinjects the sequencing reagent into that first reagent bottle 11. Inother embodiments, the number of first reagent bottles 11 may also betwo, three, four, five, six or seven, or any other numbers, depending onthe actual needs and the characteristics of each solution.

Further, the sequencing reagent allocation assembly 60 further comprisesa rinse agent bottle 67 for holding a rinse agent and a first wastebottle 68. The rinse agent bottle 67 holds a rinse agent andcommunicates with the third pump 64 via the second multi-way valve 62and the second three-way valve 63. The first waste bottle 68 holds thewaste liquid and communicates with the third pump 64 via the thirdmulti-way valve 66 and the second three-way valve 63.

When the rinse agent bottle 67 is communicated with the third pump 64via the second multi-way valve 62 and the second three-way valve 63, thethird pump 64 may extract the rinse agent in the rinse agent bottle 67to rinse the third pump 64. That is, the third pump 64 can extract andbe rinsed with the rinse agent in the rinse agent bottle 67 afterformulating one sequencing reagent and prior to formulating the nextsequencing reagent so that cross contamination between two differentgene sequencing can be avoided. When the first waste liquid bottle 68 iscommunicated with the third pump 64 via the third multi-way valve 66 andthe second three-way valve 63, the third pump 64 may inject the wasteliquid generated from rinsing into the first waste liquid bottle 68, soas to achieve the effect of environmental-friendly recycling.

In the embodiment of the present disclosure, the sequencing reagentallocation assembly 60 realizes the on-line mixing function of the fluiddevice 100. It will be appreciated that in some embodiments, the fluiddevice may also have no in-line mixing function, and accordingly, thesequencing reagent allocation assembly 60 may be omitted while stillmeeting the requirement of, and controlling, the fluid path for the basesequence determination. This simplifies the conduit path of the fluiddevice and compact the size of the sequence determination system.

In some embodiments, the fluid device 100 comprises a second containerand an imaging reagent allocation assembly 70 that includes imagingagents. When photographing samples on the first component 41 and/or thesecond component 42 using the imaging device 100, the imaging reagentallocation assembly 70 outputs the imaging reagent to the secondcontainer in communication with the valve body assembly 10. In this way,it is convenient to add the reagent for carrying out the base sequencedetermination to the first component 41 and the second component 42.

In particular, in the example of the present disclosure, the secondcontainer is the third reagent bottle 13.

In the embodiment of the present disclosure, the imaging reagentallocation assembly 70 includes a plurality of imaging reagent feedbottles 71, a fourth multi-way valve 72, a third three-way valve 73, anda fourth pump 74. The plurality of the imaging reagent feed bottles 71are used to hold a plurality of imaging reagent feed stocks. The fourthmulti-way valve 72 is conduit-connected to a plurality of imagingreagent feed bottles 71 at the same time, and conduit-connected to thethird three-way valve 73. The third three-way valve 73 is alsoconduit-connected to the fourth pump 74 and the third reagent bottle 13.The fourth pump 74 communicates with one of the imaging reagent feedbottles 71 via the third three-way valve 73 and the fourth multi-wayvalve 72. The third reagent bottle 13 communicates with the fourth pump74 via a third three-way valve 73, wherein the fourth pump 74 issequentially communicated with the plurality of imaging reagent feedbottles 71 to extract the imaging reagent stocks from the plurality ofimaging reagent feed bottles 71 for mixing and formulating an imagingreagent. The fourth pump 74 is in communication with the third reagentbottle 13 for injecting the imaging reagent into the third reagentbottle 13.

In the embodiment of the present disclosure, the plurality of imagingreagent feed bottles 71 contain different imaging reagent stocks,respectively, so that the imaging reagent stocks in the plurality ofimaging reagent feed bottles 71 can be sequentially extracted by thefourth pump 74 so as to be mixed and formulated into an imaging reagent.Specifically, the number of imaging reagent feed bottles 71 is five. Theplurality of imaging reagent feed bottles 71 may be placed on a tuberack to secure the plurality of imaging reagent feed bottles 71, whileindividually labeling the five imaging reagent feed bottles 71 tofacilitate subsequent refilling of the imaging reagent stocks and toavoid cross contamination of the imaging reagent stocks. In otherembodiments, the number of imaging reagent feed bottles 71 may also besix or eight and the like, depending on the actual needs.

The fourth multi-way valve 72 is provided in the same manner as thestructure of the first multi-way valve 20, except that the fourthmulti-way valve 72 enables the fourth pump 74 to communicate with theplurality of imaging reagent feed bottles 71 sequentially, and that thefourth multi-way valve 72 selects one of the imaging reagent feedbottles 71 to communicate, controlling the communication duration so asto control the amount adjustment of the reagent stocks extracted fromthe imaging reagent feed bottle 71 by the fourth pump 74. Therefore, itis possible to enable the proportional formulation of the imagingreagent stocks from the plurality of imaging reagent feed bottles 71 inaccordance with the sequencing requirements.

The third three-way valve 73 has a structure configured in the samemanner as the first three-way valve 30. The third three-way valve 73 canenable the communication between the fourth pump 74 and the fourthmulti-way valve 72 so that the fourth pump 74 can extract the imagingreagent stocks from the plurality of imaging reagent feed bottles 71 andformulating into an imaging reagent. The third three-way valve 73 canenable the communication between the fourth pump 74 and the thirdreagent bottle 13 so that the fourth pump 74 can inject the formulatedimaging reagent into the imaging reagent bottle 13.

The fourth pump 74 may provide a negative pressure to the plurality ofimaging reagent feed bottles 71 via the third three-way valve 73 and thefourth multi-way valve 72 to extract the imaging reagent stocks in theplurality of imaging reagent feed bottles 71. The fourth pump 74 mayalso provide a positive pressure to the third reagent bottle 13 via thethird three-way valve 73 to inject the imaging reagent into the thirdreagent bottle 13.

Further, the imaging reagent allocation assembly 70 further comprises asecond mixer 75, the second mixer 75 being connected between the thirdthree-way valve 73 and the third reagent bottle 13 and comprising aplurality of the second winding ducts 751 that are connected end to endand are in communication between the third three-way valve 73 and thethird reagent bottle 13.

The second mixer 75 has a structure configured in the same manner as thefirst mixer 65. The imaging reagent injected from the second mixer 75 bythe fourth pump 74 is buffered through the plurality of second windingducts 751 and the flow path of the imaging reagent is increased. As aresult, the plurality of imaging reagent stocks in the imaging reagentis sufficiently mixed to enhance the efficiency of the imaging reagentreaction.

Further, in some embodiments, the drive assembly 50 further includes afourth three-way valve 53, a fifth three-way valve 54, a second wastebottle 55, and a third waste bottle 56. The fourth three-way valve 53 isconduit-connected between the first pump 51 and the first component 41,while conduit-connected to the second waste bottle 55. The fifththree-way valve 54 is connected between the second pump 52 and thesecond component 42 while conduit-connected to the third waste bottle56.

The first pump 51 communicates with the first component 41 or the secondwaste bottle 55 through the fourth three-way valve 53. Therefore, it ispossible for the first pump 51 to extract the waste liquid, which hascompleted the base sequence determination, from the first component 41and then inject the waste liquid to the liquid bottle 55, so that thefirst pump 51 provides the next negative pressure to the first component41 to perform the base sequence determination. The fifth three-way valve54 has a structure configured in the same manner as the fourth three-wayvalve 53, and will not be described in details here. The third wastebottle 56 has a structure configured in the same manner as the secondwaste bottle 55, and will not be described in detail here.

In the embodiment of the present disclosure, the imaging reagentallocation assembly 70 enables the on-line mixing function of the fluiddevice 100. It will be appreciated that in some embodiments, the fluiddevice may also have no in-line mixing function, and accordingly, theimaging reagent allocation assembly 70 may be omitted. This simplifiesthe conduit path of the fluid device and compact the size of thesequence determination system.

In some embodiments, the fluid device 100 includes a first control unitthat electrically connects the valve body assembly 10 and the driveassembly 50 to control the operation of the valve assembly 10 and thedrive assembly 50. In this way, the automatic control of the valve bodyassembly 10 and the drive assembly 50 can be achieved, thereby improvingthe efficiency.

In particular, in the example of the present disclosure, the firstcontrol unit electrically connects the first multi-way valve 20, thefirst three-way valve 30, and the drive assembly 50 to control theoperation of the first multi-way valve 20, the first three-way valve 30,and the drive assembly 50. The first control unit may comprise amicrocontroller, a calculator, or a central control processor, whichcontrols the operation of the first multi-way valve 20, the firstthree-way valve 30 and the drive assembly 50 by the first control unit,thereby enabling the automatic operation of the fluid device 100 andimproving efficiency. Further, in the example of the present disclosure,the first control unit also electrically connects the second multi-wayvalve 62, the second three-way valve 63, the third multi-way valve 66,the fourth multi-way valve 72, the third three-way valve 73, the thirdpump 64 and the fourth pump 74, so that the operation efficiency of thefluid device 100 is improved.

In some embodiments, the method of controlling the base sequencedetermination further comprises: determining a plurality of setpositions when the sample on the first component 41 and/or the secondcomponent 42 is photographed using the optical device 200.

In this way, the photographing time taken by the optical device 200 canbe shortened, and the efficiency can be improved.

Specifically, the initial position for photographing the sample in thechannels of the first component 41 and the second component 42 may beinputted in the optical device 200, for example, an initial XY position,the distance to be moved each time and the number of photographing foreach channel may be set, and the base sequence determination may startfrom the initial position.

In general, each unit of the reaction device 40 includes a plurality ofchannels to expedite the sequence determination of the samples to besequenced. The sample image data of each channel consists of multiplefield of view (FOV). In one example, it is desired to photograph thesamples in the plurality of channels of the unit, so that 300 FOVs areset for each channel, and the moving position of the reaction device 40is controlled according to the set number of FOVs.

In some embodiments, referring to FIG. 3, the optical device 200includes a second control unit 202, a drive platform 204, an imageacquisition unit 206, and a light source 208. The second control unit202 transmits an initialization command and a drive command. The driveplatform 204 determines a plurality of set positions according to theinitialization command. The drive station 204 moves the reaction deviceaccording to the plurality of set positions and drive commands whenphotographing the samples on the first component 41 and the secondcomponent 42 using the optical device 200. When the drive platform 204moves the reaction device 40 to the set position, the second controlunit 202 controls the light source 208 to emit light to the firstcomponent 41 and/or the second component 42 to cause the sample toexcite the detection light, and controls the image acquisition unit 206to acquire the detection light to form image data. In this way, theautomatic control of photographing the samples on the first component 41and the second component 42 is achieved.

In particular, in some embodiments, the second control unit 202 includesan upper computer 210 used to transmit an initialization command and alower computer 212 used to transmit the drive command according to theinitialization command. When the drive platform 204 moves the reactiondevice 40 to the set position, the lower computer 212 is configured tocontrol the light source 208 to emit light to the sample to cause thesample to excite the detection light, and controls the image acquisitionunit 206 to acquire the detection light to form the image data. Theimage acquisition unit 206 is configured to directly transfer the imagedata to the upper computer 210. In this way, the number of datatransmission between the upper computer 210 and the lower computer 212can be reduced, and the image data can be directly transmitted to theupper computer 210 to enable fast sequencing.

In some embodiments, the drive platform 204 directly carries thereaction device 40 and controls the movement of the reaction device 40in the sequence determination system. The drive platform 204 includes aposition calculation unit that calculates the set position each time thereaction device 40 is moved according to the initialization command andmoves the reaction device during the sequencing process. For example, inhigh throughput sequencing, it is desired to collect the sample imagedata of a plurality of set positions in one sequencing. The drivingstage 204 calculates the set position for driving the reaction device 40every time based on the initialization command, and, upon receiving thedrive command, moving the reaction device 40 to an area where the imageacquisition unit 206 can acquire the image according to each setposition. Preferably, the drive platform 204 can enable XYZ triaxialmovement to move the reaction device 40 to the set position.

In a further embodiment, the reaction device 40 may be placed on anothersupport table, and the drive platform 204 drives the reaction device 40to the set position by driving the support table.

In some embodiments, the image acquisition unit 206 includes a camera214 to convert an optical signal into an electrical signal. In oneexample, the image acquisition unit 206 includes an optical path moduleand a camera 214. The reaction device 40 is provided on a drive platformlocated on the drive platform, on the object side of the optical pathmodule, while the camera 214 being on the image side of the optical pathmodule. The optical path module can be a microscope.

In some embodiments, the image acquisition unit 206 is configured toreceive an initialization command and turn on according to theinitialization command. As a result, the image acquisition unit 206 isturned on after the initialization, enabling the image acquisition unit206 to acquire the detection light at a faster speed.

In some embodiments, the upper computer 210 sends the initializationcommands to the image acquisition unit 206 and receives the image datatransmitted by the reception image acquisition unit 206 by a wireless orwired method. In this way, data transfer between the upper computer 210and the image acquisition unit 206 is enabled.

Specifically, the data transmission mode between the upper computer 210and the image acquisition unit 206 may be a wireless local area networktransmission, a Bluetooth transmission, or a universal serial bustransmission. Of course, in other embodiments, the present disclosure isnot limited to the above-described transmission mode, and a suitabletransmission mode may be selected according to the actual demand.

In some embodiments, the lower computer 212 includes an input/outputport for outputting a first transistor-transistor logic level signal(TLL signal) to control the light source 208 to emit light and tocontrol the image acquisition unit 206 to collect the detection light.

In this way, the lower computer 212 controls the light source 208 andthe image acquisition unit 206 through the first transistor-transistorlogic level signal, reducing the communication time of the lowerprocessor 212 with the light source 208 and with the image acquisitionunit 206, further expediting the image acquisition and enabling fastsequence determination.

Specifically, in one example, the light source 208 emits a laser of aspecific wavelength, irradiates a sample on the first component 41 andthe second component 42 so that the fluorescent group in the samplefluoresces as the detection light, which us collected by the imageacquisition unit 206 to form image data.

Further, the transistor-transistor logic level signal transmission rateis microsecond. Compared to the communication in the related art throughthe serial port, the transistor-transistor logic level signal enablesfast communication of the lower processor 212 with the light source 208and with the image acquisition unit 206, reducing the respectivecommunication time between the lower processor 212 and each component,facilitating fast sequencing. The optical apparatus 200 of theembodiment of the present disclosure may complete image acquisition at aset position when completing one cycle of sequencing, and the decreasein accumulated communication time after multiple repeats is moresignificant.

In some embodiments, when the image acquisition unit 206 acquires thedetection light, the second control unit 202 controls the light source208 to be turned off when the set exposure time of the image acquisitionunit 206 is reached. In this way, the second control unit 202 controlsthe light source 208 to emit light during the exposure time of the imageacquisition unit 206 and to turn off after the exposure, so that theimage acquired by the image acquisition unit 206 is clearer and savesenergy.

In particular, in some embodiments, the lower computer 212 controls thelight source 208 to turn off.

Further, in some embodiments, the exposure time may be set in a numberof ways, for example, by artificially setting according to thesituation, or by performing an simulated exposure process prior tosequence determination to obtain the optimal exposure time, or bycalculating the appropriate exposure time value with an algorithm. Ofcourse, in other embodiments, the exposure time is not limited to theabove-described method, and the exposure time can be set according tothe actual situation.

In some embodiments, the lower computer 212 includes an input/outputport for outputting a second transistor-transistor logic level signal tocontrol the light source 208 to be turned off.

In this way, the lower computer 212 outputs the secondtransistor-transistor logic level signal through the input/output portto turn off the light source 208, reducing the communication timebetween the lower computer 212 and the light source 208, facilitatingfast sequencing.

In some embodiments, after the light source 208 is closed, the secondcontrol unit 202 controls the drive platform 204 to move the reactiondevice 40 to the next set position to complete the acquisition of theimage data at the set position.

In this way, the optical device 200 collects images at each set positionof the reaction device 40 sequentially, thereby achieving highthroughput sequencing.

In particular, in some embodiments, after the light source 208 is turnedoff, the lower computer 212 sends the drive command again to the driveplatform 204. Further, when the acquisition of the image datacorresponding to all the setting positions is completed, the lowercomputer 212 is configured to transmit the end command to the uppercomputer 210 to complete the image acquisition of one unit of thereaction device 40.

In some embodiments, the image acquisition unit 206 is connected to theupper computer 210, and the image acquisition unit 206 transmits theimage data to a upper computer 210 at a set position, and transmits theimage data to the upper computer 210. After the light source 208 isturned off, the lower computer 212 sends the drive command to the driveplatform 204, causing the drive platform 204 to move the reaction device40 to the next set position. The lower computer 212 does not have towait for the image data transfer to complete, further shortening of thesequencing time.

In some embodiments, the drive command is a pulse signal.

In this way, the second control unit 202 transmits the drive command tothe drive platform 204 in the form of a pulse signal, reducing thecommunication time between the second control unit 202 and the driveplatform 204, facilitating rapid sequencing.

Referring to FIG. 4, in some embodiments, the image acquisition unit 206includes a focus tracking module 216 and an objective lens 218, whereinthe focus tracking module 216 controls the objective lens 218 and/or thereaction device 40 to move along the optical axis of the objective lens218 in accordance with the initialization command, so as to determinethe optimal focus position when photographing the sample using the imageacquisition unit 206. During photographing, the focus tracking module216 maintains the distance of the objective lens 218 to the samplecorresponding to the optimal focus position.

In this way, when each set position to collect image is not on the sameXY plane, the distance between the objective lens 218 and the reactiondevice 40 is adjusted by the focus tracking module 216 so that the imageacquisition unit 206 acquires clear images of the sample on different XYplanes.

In particular, in some embodiments, the distance between the objectivelens 218 and the sample is the object distance. The upper computer 210sends an initialization command to the focus tracking module 216 tocause the focus tracking module 216 to activate the auto focus trackingfunction. In one example, the movement along the optical axis of theobjective lens is considered as moving along the Z axis.

The focus tracking module 216 can control the movement of the objectivelens 218 relative to the reaction device 40 to enable clear imaging bythe camera 214 in accordance with the initialization command. Afterdetermining the camera 214 has formed a clear sample image, the focustracking module 216 performs a focus locking function. That is, when thedistance between the sample and the objective lens 218 varies with theposition of the sample to be collected, the focus tracking module 216controls the movement of the objective lens 218 to compensate for thevariation so that the sample image by the camera 214 remains clear.

Said optimal focus position corresponds to a preset distance between theobjective lens and the sample, and said preset distance may be a fixedvalue or a fixed range related to the quality of the image. In oneexample, by preliminarily defining the quality parameter of thephotograph image, the optimal focus position can be determined by thehill-climbing search algorithm so that the quality of the image taken atthe optimal focus position reaches a preset parameter.

Referring to FIG. 5, a sequence determination system 300 according to anembodiment of the present disclosure is provided, which controls thebase sequence determination. The base sequence determination comprises afirst biochemical reaction, a second biochemical reaction andphotographing, wherein the first biochemical reaction and the secondbiochemical reaction are carried out in the reaction device 40.

The sequence determination system 300 includes a control device 302, afluid device 100 and an optical device 200. The reaction device 40 isconnected to the fluid device and comprises a first component 41 and asecond component 42, wherein the first component 41 and the secondcomponent 42 carry the sample to be tested. A repeated executable unitcomprised in the base sequence determination is defined as: a secondbiochemical reaction—a first biochemical reaction—photographing

The control device 302 is configured to complete the following initialsteps, and then, when performing a second biochemical reaction and afirst biochemical reaction of the sample on one of the first component41 and the second component 42 using the fluid device 100, the opticaldevice 200 is configured to photograph the sample on the othercomponent.

The initial steps comprise:

a. the control device 302 using the fluid device 100 to perform thefirst biochemical reaction of the sample on one of the first component41 and the second component 42,

B. the control device 302 using the optical device 200 to photograph thesample on the component after the first biochemical reaction, and

c. the control device 302 using the fluid device 100 to perform thefirst biochemical reaction of the sample on another one of the firstcomponent 41 and the second component 42.

It should be noted that the explanation and demonstration of thetechnical features and benefits of the method for controlling the basesequence determination in any of the above embodiments and examples arealso applicable to the sequence determination system 300 of the presentembodiment. To avoid redundancy, it is not elaborated herein.

In some embodiments, step a and step c are carried out simultaneously,or step b and step c are carried out simultaneously, or step b iscarried out before step c, or step b is carried out after step c.

In some embodiments, the first biochemical reaction comprises anextension reaction, and the second biochemical reaction comprises groupcleavage.

In some embodiments, the extension reaction comprises simultaneouslybinding and sequencing, and simultaneously synthesizing and sequencing.

In some embodiments, the second biochemical reaction comprises capping.

In some embodiments, the photographing further comprises adding animaging reagent.

In some embodiments, referring to FIG. 2, the fluid device 100 includesa valve body assembly 10 and a drive assembly 50 that communicates withthe valve body assembly 10 through a reaction device 40. When using thefluid device 100 to perform a first biochemical reaction and/or a secondbiochemical reaction on the sample of the first component 41 and/or thesecond component 42, the valve body assembly 10 is configured to switchamong different reagents, and the drive assembly 50 causes the valvebody assembly 10 to output reagents to the first component 41 and/or thesecond component 42.

In some embodiments, the valve body assembly 10 includes a firstmulti-way valve 20 and a first three-way valve 30, the first multi-wayvalve 20 switching communication with the different reagents to thefirst three-way valve 30, the first three-way valve 30 outputs thereagent output from the first multi-way valve 20 to the first component41 and/or the second component 42.

In some embodiments, the drive assembly 50 includes a first pump 51 thatcommunicates the valve body assembly 10 through a first component 41 anda second pump 52 that communicates the valve body assembly 10 through asecond component 42. When using the fluid device 100 to perform thefirst biochemical reaction and/or the second biochemical reaction withthe sample on the first component 41 and/or the second component 42, thefirst pump 51 is configured to cause the valve body assembly 10 tooutput the reagent to the unit 41, and/or the second pump 52 isconfigured to cause the valve body assembly 10 to output the reagent tothe second component 42.

In some embodiments, the fluid device 100 includes at least one firstcontainer and sequencing reagent allocation assembly 60. The reagentcomprises a sequencing reagent. When using the fluid device 100 toperform a first biochemical reaction and/or a second biochemicalreaction on the sample of the first component 41 and/or the secondcomponent 42, the sequencing reagent allocation assembly 60 outputs thesequencing reagent to the first container in communication with thevalve body assembly 10.

In some embodiments, the fluid device 100 comprises a second containerand an imaging reagent allocation assembly 70 that includes imagingagents. When photographing samples on the first component 41 and/or thesecond component 42 using the imaging device 200, the imaging reagentallocation assembly 70 outputs the imaging reagent to the secondcontainer in communication with the valve body assembly 10.

In some embodiments, the fluid device 100 includes a first control unitthat electrically connects the valve body assembly 10 and the driveassembly 50 to control the operation of the valve assembly 10 and thedrive assembly 50.

In particular, the first control unit may receive the control signalfrom the control device 302 and control the valve assembly 10, the driveassembly 50, and other components of the fluid device 100 in accordancewith the control signal. In this way, partial function of the controldevice 302 can be implemented by the first control unit, and the load ofthe control device 302 can be reduced. In some embodiments, the firstcontrol unit and control device 302 may be integrated in a component, amodule, or a device to increase the integration of the sequencedetermination system 300 and reduce the cost.

In some embodiments, the control device 302 is configured to control theplurality of set positions of the optical device 200 when photographingthe samples on the first and/or second components.

In some embodiments, referring to FIG. 3, the optical device 200includes a second control unit 202, a drive platform 204, an imageacquisition unit 206, and a light source 208. The second control unit202 transmits an initialization command and a drive command. The driveplatform 204 determines a plurality of set positions according to theinitialization command. The drive station 204 moves the reaction device40 according to the plurality of set positions and drive commands whenphotographing the samples on the first component 41 and/or the secondcomponent 42 using the optical device 200. When the drive platform 204moves the reaction device 40 to the set position, the second controlunit 202 controls the light source 208 to emit light to the firstcomponent 41 or the second component 42 to cause the sample to excitethe detection light, and controls the image acquisition unit 206 toacquire the detection light to form image data.

In particular, the second control unit 202 may receive a control signalfrom the control device 302 and control the drive platform 204, theimage acquisition unit 206, the light source 208, and other componentsof the optical device 200 in accordance with the control signal. In thisway, the partial function of the control device 302 can be implementedby the second control unit 202, and the load of the control device 302can be reduced. In some embodiments, the second control unit 202 and thecontrol device 302 may be integrated in a component, a module, or adevice to increase the integration of the sequence determination system300 and reduce the cost.

In some embodiments, when the image acquisition unit 206 acquires thedetection light, the second control unit 202 controls the light source208 to be turned off when the set exposure time of the image acquisitionunit 206 is reached.

In some embodiments, after the light source 208 is closed, the secondcontrol unit 202 controls the drive platform 204 to move the reactiondevice 40 to the next set position to complete the acquisition of theimage data at the set position.

Referring to FIG. 4, in some embodiments, the image acquisition unit 206includes a focus tracking module 216 and an objective lens 218, whereinthe focus tracking module 216 controls the objective lens 218 and/or thereaction device 40 to move along the optical axis of the objective lens218 in accordance with the initialization command, so as to determinethe optimum focus position when photographing the sample using the imageacquisition unit 206. During photographing, the focus tracking module216 maintains the distance of the objective lens 218 to the samplecorresponding to the optimal focus position.

Referring to FIG. 5, in an embodiment of the present disclosure, acontrol device 302 for controlling base sequence determination for asequence determination system is provided. The sequence determinationsystem 300 includes a fluid device 100 and an optical device 200. Thecontrol device 302 comprises:

a storage device 304 for storing data, the data comprising a computerexecutable program; and

a processor 306 for executing a computer executable program, and saidexecuting a computer executable program comprises a method of performingany of the above embodiments.

A computer-readable storage medium according to an embodiment of thepresent disclosure is provided for storing a computer executableprogram, executing the program comprising executing the above-describedmethod in any embodiments. The computer-readable storage medium mayinclude read-only memory, random access memory, magnetic disks, oroptical disks.

In the description of this specification, the description of the terms“one embodiment”, “some embodiment”, “schematic embodiment”, “example”,“specific example”, or “some example”, means that the particularfeatures, structures, materials, or features comprised in theembodiments or examples are included in at least one embodiment orexample of the present disclosure. In the present specification, theschematic expression of the above-mentioned terminology does notnecessarily refer to the same embodiment or example. Moreover, theparticular features, structures, materials, or features described may becombined in any suitable embodiment or example in any suitable manner.

The logic and/or steps represented in the flowchart or otherwisedescribed herein, for example, may be considered as a preset sequencelist of executable instructions for implementing a logical function, maybe embodied in any computer-readable storage medium for use by aninstruction execution system, device or equipment (e.g., acomputer-based system, a system including a processor, or any othersystem that may take instructions from an instruction execution system,device or equipment and execute such instructions), or for use inconjunction with these instruction execution systems, device orequipment. For the purposes of this specification, a “computer-readablestorage medium” may be any device that may contain, store, communicate,transmit, or propagate a program for use by an instruction executionsystem, device or equipment, or for use in conjunction with suchinstruction execution systems, device or equipment. More specificexamples (a non-exhaustive list) of computer-readable storage mediaincludes the following: an electrical connection (electronic device)with one or more cabling, a portable computer disk cartridge (magneticdevice), a random access memory (RAM), a read only memory (ROM), anerasable editable read only memory (EPROM or flash memory), a fiberoptic device, and a portable compact disc read only memory (CDROM). Inaddition, the computer-readable storage medium may even be a paper orother suitable medium on which the program may be printed, which, forexample, can be optically scanned on the paper or other media, followedby editing, interpretation or, if necessary, processing in any othersuitable manner, to obtain the program electronically and then store itin a computer memory.

In addition, the functional units in the various embodiments of thepresent disclosure may be integrated in a processing module, or eachunit may be physically present independently, or two or more units maybe integrated in one module. The above-mentioned integrated module canbe implemented in the form of hardware, or can also be used in the formof software function modules. The integrated module may also be storedin a computer-readable storage medium if it is implemented in the formof a software function module and is sold or used as a standaloneproduct.

While the embodiments of the present disclosure have been shown anddescribed above, it is to be understood that the above-describedembodiments are exemplary and are not to be construed as limiting thedisclosure, and that one of ordinary skill in the art may change,modify, replace, or vary such embodiments, without departing from thescope of the disclosure.

1.-20. (canceled)
 21. A method for sequencing, comprising: loading aplurality of channels of a chip with a sample containing a nucleic acidmolecule; performing steps (i)-(iii) at least once on the sample of thechannels to determine sequence of the nucleic acid molecule, the steps(i)-(iii) comprising: (i) performing a first biochemical reaction on thesample of the channels using a fluid device connected to the chip, thefluid device comprising a valve body assembly and a drive assembly thatcommunicates with the valve body assembly via the chip, the firstbiochemical reaction comprising an extension reaction; (ii)photographing the sample on the channels after step (i) using an opticaldevice, the optical device comprising a first control unit, a driveplatform, a camera, and a light source, the first control unit includingan upper computer to transmit an initialization command and a lowercomputer to transmit a drive command according to the initializationcommand, comprising: receiving a plurality of set positions for theoptical device by the drive platform according to the initializationcommand; moving the chip by the drive platform according to theplurality of set positions and the drive command; when the driveplatform moves the chip to a set position of the plurality of setpositions, controlling the light source by the lower computer to emitlight to excite the sample to emit light for detection; imaging thesample by controlling the camera by the lower computer to acquire thelight for detection to form image data; and transferring the image datafrom the camera directly to the upper computer, without passing throughthe lower computer, to reduce data transmission between the uppercomputer and the lower computer; and (iii) performing a secondbiochemical reaction on the sample of the channels using the fluiddevice, the second biochemical reaction comprising a cleavage reaction.22. The method of claim 21, wherein the extension reaction comprisessequencing by ligation or sequencing by synthesis.
 23. The method ofclaim 21, wherein the second biochemical reaction further comprisescapping.
 24. The method of claim 21, wherein the imaging furthercomprises adding an imaging reagent.
 25. The method of claim 21, whereinwhen using the fluid device to perform the first biochemical reaction,the second biochemical reaction, or both of the sample on the channels,the valve body assembly is configured to switch connection to differentreagents, and the drive assembly allows the valve body assembly tooutput the reagent to the channels.
 26. The method of claim 25, whereinthe valve body assembly comprises a first multi-way valve and a firstthree-way valve, wherein the first multi-way valve is configured toswitch connection to different reagents to the first three-way valve,and the first three-way valve outputs the reagent output from the firstmulti-way valve to the channels.
 27. The method of claim 25, wherein thefluid device comprises at least one first container and a sequencingreagent allocation assembly, the reagent comprises a sequencing reagent,and wherein, when using the fluid device to perform the firstbiochemical reaction, the second biochemical reaction, or both of thesample on the channels, the sequencing reagent allocation assemblyoutputs the sequencing reagent to the first container communicating withthe valve body assembly.
 28. The method of claim 25, wherein the fluiddevice comprises a second container and an imaging reagent allocationassembly, the agent comprising an imaging agent, and wherein, when usingthe optical device to image the sample on the channels, the imagingreagent allocation assembly outputs the imaging reagent to the secondcontainer in communication with the valve body assembly.
 29. The methodof claim 25, wherein the fluid device comprises a second control unitthat is electrically connected to the valve body assembly and the driveassembly to control the valve body assembly and the drive assembly tooperate.
 30. The method of claim 21, wherein when the camera collectsthe light for detection, the first control unit controls the lightsource to turn off when a set exposure time of the camera is reached.31. The method of claim 30, wherein after the light source is turnedoff, the first control unit controls the drive platform to move the chipto a next set position to complete collection of the image data at theset position.
 32. The method of claim 21, wherein the camera comprises afocus tracking module and an objective lens; the focus tracking modulecontrols the objective lens, the chip, or both to move along an opticalaxis of the objective lens in accordance with the initialization commandso as to determine an optimal focus position for the camera tophotograph the sample; and wherein, when photographing, the focustracking module holds a constant distance between the objective lens andthe sample corresponding to the optimal focus position.
 33. The methodof claim 21, wherein the image data is transferred from the camera tothe upper computer via a wireless local area network transmission, aBluetooth transmission, or a universal serial bus transmission.
 34. Asystem, wherein the system comprises a control device, a fluid devicecomprising a valve body assembly and a drive assembly that communicateswith the valve body assembly via a chip, and an optical devicecomprising a first control unit, a drive platform, a camera, and a lightsource, the first control unit including an upper computer to transmitan initialization command and a lower computer to transmit a drivecommand according to the initialization command, the chip beingconnected to the fluid device; the chip comprises a plurality ofchannels, a sample being placed on the channels; the control devicebeing configured to perform following actions at least once: (i)performing a first biochemical reaction on the sample of the channelsusing a fluid device connected to the chip, the fluid device comprisinga valve body assembly and a drive assembly that communicates with thevalve body assembly via the chip, the first biochemical reactioncomprising an extension reaction; (ii) photographing the sample on thechannels after step (i) using an optical device, the optical devicecomprising a first control unit, a drive platform, a camera, and a lightsource, the first control unit including an upper computer to transmitan initialization command and a lower computer to transmit a drivecommand according to the initialization command, comprising: receiving aplurality of set positions for the optical device by the drive platformaccording to the initialization command; moving the chip by the driveplatform according to the plurality of set positions and the drivecommand; when the drive platform moves the chip to a set position of theplurality of set positions, controlling the light source by the lowercomputer to emit light to excite the sample to emit light for detection;imaging the sample by controlling the camera by the lower computer toacquire the light for detection to form image data; and transferring theimage data from the camera directly to the upper computer, withoutpassing through the lower computer, to reduce data transmission betweenthe upper computer and the lower computer; and (iii) performing a secondbiochemical reaction on the sample of the channels using the fluiddevice, the second biochemical reaction comprising a cleavage reaction.35. The system of claim 34, wherein when using the fluid device toperform the first biochemical reaction, the second biochemical reaction,or both of the sample on the channels, the valve body assembly isconfigured to switch connection to different reagents, and the driveassembly allows the valve body assembly to output the reagent to thechannels.
 36. The system of claim 35, wherein the valve body assemblycomprises a first multi-way valve and a first three-way valve, whereinthe first multi-way valve is configured to switch connection todifferent reagents to the first three-way valve, and the first three-wayvalve outputs the reagent output from the first multi-way valve to thechannels.
 37. The system of claim 35, wherein the fluid device comprisesa second control unit that is electrically connected to the valve bodyassembly and the drive assembly to control the valve body assembly andthe drive assembly to operate.
 38. The system of claim 34, wherein whenthe camera collects the light for detection, the first control unitcontrols the light source to turn off when a set exposure time of thecamera is reached.
 39. The system of claim 34, wherein after the lightsource is turned off, the first control unit controls the drive platformto move the chip to a next set position to complete collection of theimage data at the set position.
 40. The system of claim 34, wherein thecamera comprises a focus tracking module and an objective lens; thefocus tracking module controls the objective lens, the chip, or both tomove along an optical axis of the objective lens in accordance with theinitialization command so as to determine an optimal focus position forthe camera to photograph the sample; and wherein, when photographing,the focus tracking module holds a constant distance between theobjective lens and the sample corresponding to the optimal focusposition.
 41. A control device for controlling sequencing, wherein thecontrol device comprises: a storage device for storing data, the dataincluding a computer executable program; and a processor for executingthe computer executable program, wherein the executing the computerexecutable program causes performing of the method of claim 21.